Table 2.
Clusters of Orthologous Groups of Proteins (COGs) That Include Predicted Archaeal Exosome Subunits and Functionally Connected Proteins
| COG | (Predicted) function | Sequence similarity between archaeal members (E-value range) | Sequence similarity to the eukaryotic orthologs (E-value range) | The closest archaeal paralog and sequence similarity (E-value range) | Comments |
| 1097 | RNA-binding protein Rrp4p | e-40–e-25 | e-11–e-05 | COG1096; ∼e-03 | |
| 0689 | 3′-5′ exonuclease, RNase PH homolog | e80–e-60 | e-28 | COG2123; e-11–e-09 | |
| 2123 | 3′-5′ exonuclease, RNase PH homolog | e-70–e-60 | e-30 | COG0689; e-14–e-10 | |
| 1603 | Protein subunit of RNase P | e-23–0.15 | e-06–0.25 | none | The Crenarchaeal and eukaryotic proteins show limited similarity to the euryarchaeal orthologs; however, an iterative PSI-BLAST retrieves them from the database without false-positives and with high statistical significance. |
| 1369 | Protein subunit of RNase P | e-13–e-04 | ∼e-04 | none | |
| 2136 | IMP4, spliceosome subunit in eukaryotes, probably exosome subunit in archaea | e-09–0.004 | ∼e-07 | none | |
| 1382 | Prefoldin, co-translational chaperone | e-26–e-15 | ∼e-05 | COG1730; ∼0.002 | Some spurious similarities to coiled-coil domains were also detected in database searches. |
| 1325 | Uncharacterized conserved protein | e-23–e-09 | none | none | |
| 1500 | Uncharacterized conserved protein | e-72–e-46 | ∼e-20 | none | |
| 2892 | Uncharacterized conserved protein | e-07–e-05 | none | none | A newly identified COG; most of the members have not been previously annotated as proteins (Fig.2A). |
| 1096 | RNA-binding protein Cs14p | e-20–e-12 | ∼e-04 | COG1097; ∼e-03 | |
| 1487 | Predicted RNA-binding protein, PIN-domain | e-30–0.2 | none | COG1848; >0.1 | A complex COG with several paralogs in each archaeal species. |
| 1753 | Uncharacterized conserved protein | e-04–e-03 | none | none | Very distant similarity was detected between the members of this COGs and prefoldins; together with similar size and predicted α-helical structure, this might indicate a genuine evolutionary and functional relationship. |
| 2386 | Uncharacterized conserved protein | e-09–e-04 | none | none |
